Glossary Cell Cycle

26 july 2006

B-period
time period when the cell is not replicating DNA. This happens when the cell mass is lower than the initiation mass. Color in the graph: green.

C-period
time needed by a replisome (bifurcation point) to travel from the origin to the terminus, i.e. to duplicate the entire chormosome. Color in the graph: red.

Cell division
The moment when a cell divides in two separate daughter cells.

DNA
Information carrier. In this simulation, DNA contents is expressed in units of 1 genome.

D-period
time needed by the cell after termination of DNA replication until it is able to divide.
Color in the graph: blue.

E=Eclipse
Minimum time between two successive initiations. In the simulation program, this value is expressed relative to the C period. Example: E/C = 0.5 means that no new initiation can take place before half of the chromosome is replicated. (We use C=C1 before transition and C=C2 after transition).

Genome
The totality of genetic information belonging to the cell.

Growth
growth of the cell mass is typically exponential, and appears in the plot as a sawtooth pattern due to logarithmic y axis (indicated on the lefthand side).
The increase in amount of DNA (replication rate) is typically linear; in the graph, a linear y-axis is used (indicated on the righthand side).

Growth rate
growth rate is characterized by the rate at which the cell mass doubles. It is the inverse value of the doubling time Td.

Initiation mass
The minimum cell mass necessary to allow the initiation of the replication process. When the growing cell passes this threshold, an initiation of replication is triggered. However, if the eclipse is still in effect, the initiation is postponed until after the eclipse.

M
see Mass

Mass
relative cell mass. In canonical situation (after resetting the simulation), a new-born cell has mass M=1. Mass can also be seen as volume.

Mi
see Initiation mass

Multifork replication
This occurs when a cell initiates DNA replication while a previous round of replication still exists, i.e. when Td < C.

N period
Time period between end of chromosome replication and nucleoid segregation. In the plot, the end ot the N period is indicated as a white dot inside the blue D-period.

Nucleoid segregation
Bidirectional movement of DNA daughter strands which causes the separation of the nucleoids

nNucs
Number of (separated) nucleoids in the cell

oriC
origin of replication. In the simulation, oriCs indicates the number of "left tree ends" in the forking panel.

Overlap
phenomen where replication of the chromosome is performed at several locations

Replication
reproduction of DNA at a bifurcation point.

Segregation
see nucleoid segregation

terC
terminus of replication. In the simulation, terCs indicates the number of "right tree ends" in the forking panel.

Td
Doubling time, the time needed to double the cell mass. Same as greek tau.

Termination
End of a round of DNA replication, when a replisome has reached terC.

Transition
Intermediate period between steady states of growth obtained by nutritional changes (shift up/down or step up/down) or mutation.
In the plot, the transition is indicated by gray background color. During the transition, a new equilibrium is approached. Parameter indices 1 and 2 are used to indicate before or after transition, example:
Td1 = doubling time before transition,  Td2= doubling time after transition.
After a simple temperature shift, the cell switches immediately to the new state.